Wednesday, 30 June 2010

Gene patents - stifling innovation?

There have been a couple of events that have spurred me into voicing my own opinions with regard to gene patenting. The first is the Myriad gene patent of BRCA1 and BRCA2 which was overturned some weeks ago, and is now being contested (hardly a surprise when there is such a monetary incentive!). The other is an interview with ex-UK HGP director, John Sulston, in which he lays out his own concerns about gene patenting. We have to remember he was around at the start of the idea of being able to patent a gene or genome, when Craig Venter started up Celera in a bid to beat the public sequencing effort to the prize, and thus charge researchers for the privilege of accessing our own genomes.

I’m a fan of open access and transparency in science, in fact I would go so far as to say that it is a necessity of good scientific practise, and upholds and empowers the scientific method and the concept of science itself. So the idea of patenting a gene, or its specific variants, which was not invented, and is present in numerous persons within a given population, is anathema to the open access and transparent nature of good scientific practise. It prevents researchers from unhindered research into the mechanisms of mutations within the gene in question, and the ability to use it for clinical applications, such as diagnostic indicators in disease, or as prognostic indicators of therapeutic response or adverse side effects.

This is one of the major problems that can crop up when some of the drivers of pharmacological research have financially vested interests, as is the case with Myriad and other pharmaceutical companies. Don’t get me wrong, this isn’t a dig at BigPharma, it’s a dig at the money-grabbers, bureaucrats and lawyers for thinking they could ever place a patent on a naturally occurring biological molecule. If they are going to patent something to protect their intellectual property, do it in a responsible manner that does not stifle progress and innovation in the name of financial gain. Patent the diagnostic test and specific protocol itself if needs be; surely that protects their intellectual property sufficiently?

Now, I’m not a patent lawyer (I once heard a talk given by a chap going through the training, I wouldn’t want to subject myself to that level of tedium and mind-numbing law-talk, despite the excellent remuneration), so I don’t know the inner-workings of patent law, and the loop holes and requisites required, but the Myriad patent case and others in Australia need to set a precedent that naturally occurring biological molecules, complexes and machinery are not patentable, and that any artificial or derived variations on the natural theme are shown to be, with sufficient supporting evidence, sufficiently different that they are unlikely to exist, or occur within nature itself.

That should rule out any unscrupulous companies trying to patent rare variants too.

I understand the importance of patents, I believe (correct me if I’m wrong here), the patent offices were originally set up to promote innovation whilst protecting the rights of the inventors themselves. So we need to keep that original basis in mind when we consider the patenting of biological materials. Will this patent promote, or stifle, innovation?

Gene patenting can only ever stifle innovation that arises from competition, thus it is untenable, and should be rejected outright.

Sunday, 27 June 2010

The Weekly Round-Up

This week there have been several stories of note that I've not had time to blog about, so I thought I'd start a weekly round-up of interesting news pieces.

[1] Starting with the Sanger Institutes announcement of their own 10,000 genomes project. The WTSI is performing its own 10,000 genomes project, its aim to help uncover the various genetic elements that predispose to various diseases and disorders by full resequencing of 4,000 individuals, and the exomes of another 6,000.

[2] This announcement from the WTSI comes in the same week that the original 1000 genomes project announces its release of their pilot data, prior to the start of their database for public and research use.

[3] I've already covered this story, but it seems, to me at least, a step forward towards the implementation of clinical sequencing by the Royal Brompton Hospital

[4] An interview with Francis Collins in The Times about how he sees the future of genomic medicine panning out, with an emphasis on the hurdles still to overcome, including the education of physicians and the general public about personal genomics and personalized medicine.

[5] 23andMe have published their first paper in PLoS Genetics, a GWAS of various phenotypic traits. Whilst most of these may seem superficial (hair colour, eye colour, etc), it is their research framework that is the focus of this paper.

[6] Its 10 years since Craig J. Venter and Francis Collins stepped out on the White House Lawn with President Bill Clinton to announce the complete draft of the Human Genome.

There has been much speculation about the predicted impact of genomic medicine, and whether or not it has, or will be able to, deliver on all its promises. It's true that most of the general public won't have noticed the significant advances made in genomic medicine, but I think we are within 10 years of routine clinical sequencing and the start of an era in personalized medicine. Watch this space!

Thursday, 24 June 2010

Celebrating 10 years since the completion of the Human Genome Project

A new programme has begun on BBC Radio 4 called "The Age of the Genome" as a part of the 10 year anniversary of the completion of the the Human Genome Project. This ~30 mins programme is narrated by the Evolutionary biologist, and champion of public understanding of science, Richard Dawkins. Whilst most people will be aware of Prof. Dawkins for his some what vocal criticism of religion, he stands out in my mind as man who's priorities are what he calls "concious raising". This doesn't just apply to the criticisms of religion, but also, and far more importantly, to increasing the general publics understanding and appreciation of the work carried out by hard working physicians and scientists around the globe. In particular his book, The Selfish Gene, a book that for me had a large impact on my initial understanding of genetics during the first year of my undergraduate studies.

The programme itself is largely made up of interviews with the principle players in the Human Genome Project; Francis Collins, John Sulston, Craig Venter and sound bites from other emninent scientists, including James Watson. For those not familiar with any of these names, or only a passing familiarity, Francis Collins is the current director of the US National Institute of Health and one of the heads of the HGP. Craig Venter is a more household name, particularly in recent weeks with the construction of a cell with an entirely synthetic genome which has raised so much debate. John Sulston headed up the UK branch of the HGP based at the Wellcome Trust Sanger Institute in Cambridge, UK. And finally James Watson, one of the co-discoverers of the 3D structure of DNA, alongside the late Francis Crick and Rosalind Franklin.

The programme describes the process of Sanger sequencing, the technique that made possible the completion of the human genome, alongside other computational technological advances, including accurate sequence alignment and sequence construction. As is likely with any science programme involving RD, there is a discussion of the evolutionary implications of the HGP, including the comparisons with the nematode worm, Caenorhabditis elegans, and the surprising finding that our genome only contains ~20,000 genes (the current count from the 1,000 Genomes project is 21,370).

I'm personally looking forward to the continuation of this radio series, whilst it may not necessarily be a steep learning curve for myself, it will certainly give me invaluable hints into how to present scientific advances to the lay audience.

Episode one can be listened to below in the embeded player, or directly from the BBC Radio 4 Website.

Wednesday, 23 June 2010

Clinical Sequencing in the UK

It would appear that one of the first exome-sequencing projects run by the NHS is being launched at the Royal Brompton Hospital in London. Their aim appears to be to associate rare and common variants with cardiomyopathies and the results of MRI scans.

This is quite a leap forward for clinical sequencing, but I wonder whether they may be a little premature? The costs of sequencing have been plummeting for the last decade, but the current technologies have their own cons as well as pros. Sure they're faster and generally more high-throughput; but they also generate shorter read lengths and are thus more prone to sequencing errors which makes in depth sequencing a must for accurate data requisition. Then there is the computational analysis and storage requirements. Next-gen sequencers generate Gb of data and require specific bioinformatic tools to deal with sequence alignment because of the short read length, as well as the IT infrastructure to deal with the sudden explosion in data quantity; 10,000 exomes is a lot of information to handle and store. I can only assume they have these tools and expertise in place. What of the variants that are not known to be associated with cardiac defects, yet predispose to it nonetheless? Are they going to assess these as well. Their press release talks of tailoring each patients treatment to their genotype - that is premature!

The pros are just as numerous as the cons. Complete exome-sequencing will be able to uncover the rare variants that are most likely to have a high impact on disease risk and severity. They will be able to compare high resolution imaging directly with genotypic data, as well as other clinical and phenotypic information collected by the medical staff. This project may well set a precedent for clinical sequencing in the UK if the predicted results are as spectacular as they could be. Oh and they are looking for volunteers, preferably ones with a family history of cardiomyopathy. If it weren't all the way down in London I'd be tempted to give it a whirl, as long as I could get a copy of the data back for myself - cheaper than DTC testing!

I will be intrigued to see what comes of this project. I personally wouldn't have predicted routine clinical sequencing for another 20 years, perhaps the Royal Brompton Hospital researchers might be able to bump that forward a little.

Edit: Royal Brompton Hospital Press Release

Sunday, 20 June 2010

Rare variants contribute to autoimmune diseases

Genome-wide association studies (GWAS) were hailed as a landmark change in the way genetics was carried out; finally there was a tool that could be used to probe the genetics of common complex diseases based upon the common disease-common variant hypothesis. For those not familiar with this idea it was hypothesised that susceptibility to common diseases was likely influenced by multiple genetic variants that were generally common amongst the populace. People who have a disease may have multiple variants, but at the same time some people may also have these variants and never suffer from a given disease; there were key environmental triggers. Either way scientists would be able to uncover these variants and hopefully use them to predict who might suffer from a disease, or else use them to predict the severity.

A major GWAS was published by the Wellcome Trust Case-Control Consortium back in 2007 that covered seven common diseases and utilised a cohort of common controls to test against each disease. Needless to say multiple variants were detect, all with rather modest effects. Since its publication the WTCCC associations have been replicated and validated, and new variants have also been detected that are associated with risk of a number of common diseases, including rheumatoid arthritis, prostate cancer, cardiovascular disorders and more. My own interests lie in the field of autoimmunity, developed when I was on my undergraduate work placement. It soon became obvious that if these common variants did truly increase a persons risk of developing disease then it would involve the complex interactions of multiple pathways and multiple tissue and cell types - that's a needle in an Atlantic ocean of needles to put it lightly.

So the question is do common variants actually increase a persons risk of developing a given disease that is associated with it? Based on the evidence so far I'd say that this may well be the case, but, and this a very important but, not all of them. A paper published last year simulated the effects of rare variants in linkage with associated common variants and showed how they could potentially inflate the frequency of common variants to the point where they reach genome-wide statistical significance. Now I wont pretend to fully understand this paper in question, but I do understand the potential implications; rare variants may have a role to play in disease risk, and GWAS are not the tool to uncovering those variants.

So why am I even talking about this. Most people in the genetics community will be more than aware of the current grumblings and misgivings about GWAS. The reason is this paper published online in Nature this week:

Surolia et al, (2010) Functionally defective germline variants of sialic acid acetylesterase in autoimmunity, Nature Advanced Online publication doi:10.1038/nature09115

Nature News has coverage of this article, and explains things very concisely, but I'd still like to have a go at my own coverage (after all its good practise for when I start my PhD in October).

The justification for investigating this particular gene, SIAE, is due to previous functional work on siae mutant mice which display a defect in B-cell tolerance. They hypothesise that potentially variants in the human SIAE gene may contribute to autoimmunity, despite no variants within this gene having been associated by GWAS. In essence this is a good old-fashioned hypothesis driven candidate-gene approach.

They re-sequenced the SIAE exons (10 in total) in a number of autoimmune patients of European ancestry and detected 2 rare variants, one in a patient with rheumatoid arthritis and another in a patient with Crohn's disease. They then extended their re-sequencing efforts to include a total of 188 cases and 190 controls and uncovered a number of point mutations, including previously characterised single nucleotide polymorphisms (SNPs). This cohort was then extended to 923 autoimmune cases (varying autoimmune conditions including RA, type 1 diabetes, systemic lupus erythematosus and inflammatory bowel disease, amongst others). 14 previously uncharacterised SNPs were detected in the initial phase, including several cases homozygous for a non-synonymous mutation M89V. In their control cohort of 648 volunteers they detect 17 people carrying one of 8 non-synonymous SNPs, none of which were homozygous for the M89V variant.

The next step was to determine whether variants were defective in either their catalytic activity or secretion. They generated FLAG-tagged cDNA constructs for each variant using site-directed mutagenesis and transfected them in (at least) triplicate into HEK-293T cells in order to quantify protein levels by quantitative western blotting and an esterase activity assay. To cut a long story short 24 of the 923 subjects carried catalytically defective alleles, described as an activity 50% below that of the wild-type. Others had a profound defect in secretion. Amongst the secretion defective alleles was the previously mention 89V allele which retained catalytic activity, but whilst detected in 9.7% of controls in the heterozygous state, only cases were found to be homozygous for this mutation suggesting a recessive mechanism for this particular allele. In addition only cases displayed statistically significant departure from Hardy-Weinberg expectations, thus the 89V variant is enriched in patients suffering from autoimmune conditions.

The other alleles were detected for a dominant-negative effect by inhibition of the wild-type in a Murine-based assay, seven of which were classed as such.

So we start to see a picture building of multiple rare variants being detected in autoimmune patients that have loss of function mechanisms, and thus may play a role in the aetiology of these diseases. But, wait, we aren't finished yet. This was a rather comprehensive paper. Only one of 11 catalytically defective variants wasn't conserved between primates and rodents, thus providing further evidence of the impact of these variants.

So how much do these variants contribute to autoimmune disease? This is where the odds ratios come in. Surolia et al calculated OR for a number of disorders, including RA and type 1 diabetes. The verdict? RA OR 8.31 (95%CI=1.69-40.87) and type 1 diabetes OR 7.89 (95%CI=1.58-39.30). So we see that they span quite a large range, but significantly none of the 95% confidence intervals fall below 1.0, so there is a genuine effect on disease. The large ranges are most likely due to interactions with other loci, stochastic variation, different effect sizes for each variant, in other words the complexity of the disease modulates the effect of a given variant. Overall they compute their OR for all autoimmune conditions as 8.62 (95%CI=2.03-36.62).

These are pretty significant findings, particularly with respect to my own disease of interest, rheumatoid arthritis. Previous associations from GWAS haven't detected risk ratios for any variants above 1.2-1.6. The only known variants to exceed such odds ratios are those of the shared epitope variants which account for about 20-30% of RA genetic susceptibility. In short, this is a big finding. It is, however, not the end of the story. This is just a snap-shot of the rare variants associated with autoimmunity in one particular gene, the question is, can this approach be extended to try and find the other variants that affect disease risk?

My opinion as a lowly student? It is highly likely that rare variants contribute much more to common diseases than was previously thought, but finding them is going to require some new tools. What about all those common variants associated with disease? How do we find the causal variants? Well the answer is at the beginning of this paper by Surolia et of associated regions in cases and controls. They show in their power calculations that to reach a power or 0.8 they require 550 cases and 550 controls, that is a hell of a lot easier to achieve than the predicted 10,000+ cases and controls predicted to detect the most modest odds ratios using the GWA approach.

But there are other implications to think of too, notably those of costs. GWAS require multi-centre collaborations (granted this study did too), but they also require the use of thousands of micro array chips to genotype the entire genome, and even then there are certain areas that are notably missing (I'm thinking of the FCGR locus here which is badly represented on whole-genome chips because of its copy number polymorphic state and the high homology between the genes at this locus). These are very expensive studies to carry out and utilise some very complex mathematics I'm not even going to pretend to understand. So it seems that studies such as this may turn out to be more cost-effective, but only if they produce results on this scale. Seems like a tricky situation, common variants and GWAS versus rare variants and candidate gene approaches.

I've still not answered the whole question though. Re-sequencing studies are being carried out as follow-up to associated regions, but that still leaves those areas that may be implicated, but are not candidate regions. In all honesty I can't say what the answer is, but I'm hoping that the genetics community will come up with an answer sometime, sooner rather than later. All I do know is that this paper may well set the stage for more investigations into the role of rare variants in autoimmunity and other complex disorders.

Dickson et al (2010) Rare Variants Create Synthetic Genome-Wide Associations. PLoS Biol 8(1): e1000294. doi:10.1371/journal.pbio.1000294

Wellcome Trust Case Control Consortium (2007)
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls, Nature 447, 661-678

Surolia et al, (2010) Functionally defective germline variants of sialic acid acetylesterase in autoimmunity, Nature Advanced Online publication doi:10.1038/nature09115

Friday, 18 June 2010

Kooky genomics

News released this week reveals that the personal genomics company Knome are going to persue the sequencing of Black Sabbath's ex-front man Ozzy Osbourne genome. Their justification? To find out why, after 40+ years of alcohol and narcotic abuse, the man is still alive!

What are they expecting to find? Mutations leaping out left, right and centre? This seems like a bit of a publicity stunt, but their justification for using extreme medical cases is a valid one. However, when n=1 they might struggle to really pin down what it is that has allowed the Brummy rocker to survive so damn long.

This could reveal some very interesting aspects of Ozzy's biology, or alternatively it could reveal that actually it's a little bit more complicated than they thought it would be (sorry to Ben Goldacre, I've been gagging to use that line).

FDA cracks down on DTC genetic testing

There's hardly a genetics blog about that hasn't reported this news already, but I thought I'd jump on the bandwagon and chime in with my 2 pence. The fact of the matter is that letters have been issued to several DTC genetic testing companies; 23andMe Inc, deCode Genetics, Knome Inc, Navigenics, and Illumina, in which they have been asked to submit their genetic testing for review by the FDA. The FDA have justified their actions by stating from the companies websites, which they claim are used as medical diagnostics. In particular with respect to pharmacogenetic markers of Warfarin and clopidogrel that are tested by 23andMe:

23andMe has never submitted information on the analytical or clinical validity of its tests to FDA for clearance or approval. However, your website states that the 23andMe Personal Genome Service™is intended to tell patients in advance how they will respond to certain medications including warfarin and clopidogrel. It also states that the data generated from the 23andMe Odds Calculator, a feature ofthe 23andMe Personal Genome Service™, includes the contribution of single-nucleotide polymorphisms (SNPs) to disease risk. Consumers may make medical decisions in reliance on this information.

Each company has been selected based on the various services they offer, but for me there it seems that their action can be called into question for several reasons. The first is the recent sample mix-up from 23andMe last week. Some may see the FDA's actions as reactionary and PR-motivated, afterall it is not a matter of whether DTC genetics are used for medical purposes. Nor would their registration as such prevent such mix-ups. I trust that all of these personal genetics companies have strict quality control measures in place becuase of the potentially sensitive information they are dealing with.
The second point is that, whilst I agree DTC genetics needs to be regulated, it should not be as medical diagnostics. Unless people are suddenly using this information to self-medicate then it is not being used for the purposes that the FDA state.

What the FDA should be doing is setting up a division for DTC regulation to prevent the sham-companies from scheming money out of the unwitting public and setting the standards for future personal genomics companies.

This could potentially damage personal genomics if the FDA handle it badly. If I were the CEO's of these DTC companies I would perhaps propose a compromise so that the proper, and appropriate regulation can be implemented; one that does not place personal genetics under the misnomer of medical diagnostics.

Thursday, 17 June 2010

The opening post

Thanks to Drew Conway over at ZIA, I've been inspired to finally start up a blog that isn't just full of my inane ramblings (well mostly anyway). I've often had sudden urges to start writing about my passion of genetics, but I've finally been convinced that this is actually going to be of some benefit. Drew gives 10 great reasons why grad students should blog, and I have to admit the view the faculty had of bloggers was one of my personal barriers. Why was it a barrier? It shouldn't have been because I don't even know their opinions! More fool me.

So here is my attempt to blog and write about my passion for genetics, and hopefully use it as a platform to test ideas, wax lyrical (I promise not too much), but also to help hone my critical thinking skills.